Photo Quiz: A 34-Year-Old Man from Cameroon with Gastrointestinal Bleeding and Syncope [Photo Quiz]
(Source: Journal of Clinical Microbiology)
Source: Journal of Clinical Microbiology - July 26, 2019 Category: Microbiology Authors: Manski, S. A., OBrien, J. J., Patel, D. M. Tags: Photo Quiz Source Type: research

Improving the Laboratory Information System: a Micro-Comic Strip [Editorial]
(Source: Journal of Clinical Microbiology)
Source: Journal of Clinical Microbiology - July 26, 2019 Category: Microbiology Authors: McAdam, A. J. Tags: Editorial Source Type: research

Cross-Reactivity Using Chimeric Trypanosoma cruzi Antigens: Diagnostic Performance in Settings Where Chagas Disease and American Cutaneous or Visceral Leishmaniasis Are Coendemic [Immunoassays]
Chimeric T. cruzi antigens have been proposed as a diagnostic tool for chronic Chagas disease (CD) in both settings where Chagas disease is endemic and those where it is not endemic. Antibody response varies in accordance to each T. cruzi strain, presenting challenges to the use of antigens lacking demonstrated cross-reactivity with Leishmania spp. Our group expressed four chimeric proteins (IBMP-8.1, IBMP-8.2, IBMP-8.3, and IBMP-8.4) and previously assessed their diagnostic performance to determine cross-reactivity with Leishmania spp. Here, we validated our findings using serum samples from different Brazilian geographic...
Source: Journal of Clinical Microbiology - July 26, 2019 Category: Microbiology Authors: Daltro, R. T., Leony, L. M., Freitas, N. E. M., Silva, A. A. O., Santos, E. F., Del-Rei, R. P., Brito, M. E. F., Brandao-Filho, S. P., Gomes, Y. M., Silva, M. S., Donato, S. T., Jeronimo, S. M. B., Monteiro, G. R. d. G., Carvalho, L. P., Magalhaes, A. S., Tags: Immunoassays Source Type: research

Multiplex Real-Time PCR-shortTUB Assay for Detection of the Mycobacterium tuberculosis Complex in Smear-Negative Clinical Samples with Low Mycobacterial Loads [Mycobacteriology and Aerobic Actinomycetes]
In this study, we evaluated the performance of this novel multiplex assay for detecting the MTBC in comparison with that of the conventional culture-based method. The multiplex real-time PCR-shortTUB assay targets two genes, whiB3 (redox-responsive transcriptional regulator) and pstS1 (phosphate-specific transporter), yielding limits of detection (LOD) of 10 copies and 100 copies, respectively, and amplification efficiencies of 92% and 99.7%, respectively. A total of 94 extrapulmonary samples and pulmonary samples with low mycobacterial loads (all smear negative; 75 MTBC culture positive) were analyzed using the test, yiel...
Source: Journal of Clinical Microbiology - July 26, 2019 Category: Microbiology Authors: Alcaide, F., Trastoy, R., Moure, R., Gonzalez-Bardanca, M., Ambroa, A., Lopez, M., Bleriot, I., Blasco, L., Fernandez-Garcia, L., Tato, M., Bou, G., Tomas, M., Mycobacterial and GEMARA SEIMC/REIPI Bacterial Clinical Adaptation Study Group Tags: Mycobacteriology and Aerobic Actinomycetes Source Type: research

Biographical Feature: Rebecca Lancefield, Ph.D. [Biographical Feature]
(Source: Journal of Clinical Microbiology)
Source: Journal of Clinical Microbiology - July 26, 2019 Category: Microbiology Authors: Carroll, K. C. Tags: Biographical Feature Source Type: research

Alternate Nucleic Acid Targets Can Be Used To Create a Composite Standard To Evaluate Clinical Performance of Nucleic Acid Amplification Tests [Commentary]
Evaluating the clinical performance of a new nucleic acid amplification test (NAAT) for Mycoplasma genitalium, B. Kirkconnell, B. Weinbaum, K. Santos, T. Le Nguyen, et al. (J Clin Microbiol 57:e00264-19, 2019, https://doi.org/10.1128/JCM.00264-19) created 3 alternate NAATs that detected other unique M. genitalium gene targets. Lacking a reference standard, they used the consensus of results with those 3 NAATs as the comparator. This approach could be a new paradigm to evaluate new NAATs when there is no previously defined reference standard. (Source: Journal of Clinical Microbiology)
Source: Journal of Clinical Microbiology - July 26, 2019 Category: Microbiology Authors: Schachter, J., Chernesky, M. Tags: Commentary Source Type: research

Prospective Cohort Study on Performance of Cerebrospinal Fluid (CSF) Xpert MTB/RIF, CSF Lipoarabinomannan (LAM) Lateral Flow Assay (LFA), and Urine LAM LFA for Diagnosis of Tuberculous Meningitis in Zambia [Mycobacteriology and Aerobic Actinomycetes]
Tuberculous meningitis (TBM) is a devastating infection of the central nervous system lacking an adequate point-of-care diagnostic test. We conducted a prospective cohort study of 550 Zambian adults with suspected TBM to determine the diagnostic accuracy of cerebrospinal fluid (CSF) Xpert MTB/RIF, CSF lipoarabinomannan (LAM), urine LAM, CSF total protein, and CSF glucose compared with the gold standard of CSF culture. We categorized patients with a positive CSF tuberculosis (TB) culture as definite TBM. We also assessed inpatient and 1-year mortality on definite TBM patients when CSF Xpert MTB/RIF results were available in...
Source: Journal of Clinical Microbiology - July 26, 2019 Category: Microbiology Authors: Siddiqi, O. K., Birbeck, G. L., Ghebremichael, M., Mubanga, E., Love, S., Buback, C., Kosloff, B., Ayles, H., Atadzhanov, M., Dheda, K., Koralnik, I. J. Tags: Mycobacteriology and Aerobic Actinomycetes Source Type: research

Development of Broth Microdilution MIC and Disk Diffusion Antimicrobial Susceptibility Test Quality Control Ranges for the Combination of Cefepime and the Novel {beta}-Lactamase Inhibitor Enmetazobactam [Bacteriology]
Third-generation cephalosporin resistance among Enterobacteriaceae, mediated by the spread of extended-spectrum β-lactamases (ESBLs), is a very serious medical concern with limited therapeutic options. Enmetazobactam (formerly AAI101) is a novel penicillanic sulfone β-lactamase inhibitor active against a wide range of ESBLs. The combination of enmetazobactam and cefepime has entered phase 3 development in patients with complicated urinary tract infections. Using the Clinical and Laboratory Standards Institute (CLSI) M23 tier 2 study design, broth microdilution MIC and disk diffusion quality control (QC) ranges we...
Source: Journal of Clinical Microbiology - July 26, 2019 Category: Microbiology Authors: Belley, A., Huband, M. D., Fedler, K. A., Watters, A. A., Flamm, R. K., Shapiro, S., Knechtle, P. Tags: Bacteriology Source Type: research

Treponema pallidum Nucleic Acid Amplification Testing To Augment Syphilis Screening among Men Who Have Sex with Men [Bacteriology]
Syphilis rates in much of the world are now at their highest levels in almost three decades, and new approaches to controlling syphilis, including diagnostic tests with shorter window periods, are urgently needed. We compared the sensitivity of syphilis serological testing using the rapid plasma reagin (RPR) test with that of the combination of serological testing and an experimental 23S rRNA Treponema pallidum real-time transcription-mediated amplification (TMA) assay performed on rectal and pharyngeal mucosal swabs. T. pallidum PCR assays for the tpp47 gene were performed on all TMA-positive specimens, as well as specime...
Source: Journal of Clinical Microbiology - July 26, 2019 Category: Microbiology Authors: Golden, M., ODonnell, M., Lukehart, S., Swenson, P., Hovey, P., Godornes, C., Romano, S., Getman, D. Tags: Bacteriology Source Type: research

Carbapenem-Nonsusceptible Pseudomonas aeruginosa Isolates from Intensive Care Units in the United States: a Potential Role for New {beta}-Lactam Combination Agents [Epidemiology]
Pseudomonas aeruginosa, a frequent pathogen in the intensive care unit (ICU), has the propensity to develop antibiotic resistance. In particular, carbapenem-nonsusceptible (NS) P. aeruginosa poses tremendous challenges, and new antibiotics will be needed to treat this phenotype. Here we determine carbapenem nonsusceptibility rates for contemporary P. aeruginosa isolates from U.S. ICUs and in vitro activities of new β-lactam combination agents. Between July 2017 and June 2018, consecutive nonduplicate P. aeruginosa isolates from blood and respiratory tract sources were recovered from patients admitted to the ICUs of 36...
Source: Journal of Clinical Microbiology - July 26, 2019 Category: Microbiology Authors: Asempa, T. E., Nicolau, D. P., Kuti, J. L. Tags: Epidemiology Source Type: research

GenoType NTM-DR Performance Evaluation for Identification of Mycobacterium avium Complex and Mycobacterium abscessus and Determination of Clarithromycin and Amikacin Resistance [Mycobacteriology and Aerobic Actinomycetes]
We evaluated the GenoType NTM-DR (NTM-DR) line probe assay for identifying Mycobacterium avium complex (MAC) species and Mycobacterium abscessus subspecies and for determining clarithromycin and amikacin resistance. Thirty-eight reference strains and 145 clinical isolates (58 MAC and 87 M. abscessus isolates), including 54 clarithromycin- and/or amikacin-resistant strains, were involved. The performance of the NTM-DR assay in rapid identification was evaluated by comparison with results of multigene sequence-based typing, whereas performance in rapid detection of clarithromycin and amikacin resistance was evaluated by comp...
Source: Journal of Clinical Microbiology - July 26, 2019 Category: Microbiology Authors: Huh, H. J., Kim, S.-Y., Shim, H. J., Kim, D. H., Yoo, I. Y., Kang, O.-K., Ki, C.-S., Shin, S. Y., Jhun, B. W., Shin, S. J., Daley, C. L., Koh, W.-J., Lee, N. Y. Tags: Mycobacteriology and Aerobic Actinomycetes Source Type: research

Proficiency Testing of Virus Diagnostics Based on Bioinformatics Analysis of Simulated In Silico High-Throughput Sequencing Data Sets [Virology]
Quality management and independent assessment of high-throughput sequencing-based virus diagnostics have not yet been established as a mandatory approach for ensuring comparable results. The sensitivity and specificity of viral high-throughput sequence data analysis are highly affected by bioinformatics processing using publicly available and custom tools and databases and thus differ widely between individuals and institutions. Here we present the results of the COMPARE [Collaborative Management Platform for Detection and Analyses of (Re-)emerging and Foodborne Outbreaks in Europe] in silico virus proficiency test. An art...
Source: Journal of Clinical Microbiology - July 26, 2019 Category: Microbiology Authors: Brinkmann, A., Andrusch, A., Belka, A., Wylezich, C., Höper, D., Pohlmann, A., Nordahl Petersen, T., Lucas, P., Blanchard, Y., Papa, A., Melidou, A., Oude Munnink, B. B., Matthijnssens, J., Deboutte, W., Ellis, R. J., Hansmann, F., Baumgär Tags: Virology Source Type: research

Suggested Modifications To Improve the Sensitivity and Specificity of the 2010 CDC-Recommended Routine Streptococcus agalactiae Screening Culture for Pregnant Women [Letter To The Editor]
(Source: Journal of Clinical Microbiology)
Source: Journal of Clinical Microbiology - July 26, 2019 Category: Microbiology Authors: Salimnia, H., Robinson-Dunn, B., Gundel, A., Campbell, A., Mitchell, R., Taylor, M., Fairfax, M. R. Tags: Letter To The Editor Source Type: research

Bacterial Genotyping of Central Nervous System Tuberculosis in South Africa: Heterogenic Mycobacterium tuberculosis Infection and Predominance of Lineage 4 [Mycobacteriology and Aerobic Actinomycetes]
In this study, we set out to determine whether a certain M. tuberculosis lineage demonstrated tropism to cause TBM in patients from Cape Town, South Africa. DNA was extracted from formalin-fixed paraffin-embedded central nervous system (CNS) tissue from a unique neuropathological cohort of 83 TBM patients, collected between 1975 and 2012. M. tuberculosis lineages 1, 2, 3, and 4 were determined using an allele-specific PCR and Sanger sequencing. Of the 83 patient specimens tested, bacterial characterization could be performed on 46 specimens (55%). M. tuberculosis lineage 4 was present in 26 patient specimens (56%), and non...
Source: Journal of Clinical Microbiology - July 26, 2019 Category: Microbiology Authors: van Leeuwen, L. M., Versteegen, P., Zaharie, S. D., van Elsland, S. L., Jordaan, A., Streicher, E. M., Warren, R. M., van der Kuip, M., van Furth, A. M. Tags: Mycobacteriology and Aerobic Actinomycetes Source Type: research

Invasive Pneumococcal Disease and Influenza Activity in a Pediatric Population: Impact of PCV13 Vaccination in Pandemic and Nonpandemic Influenza Periods [Epidemiology]
The objective of this study was to analyze the incidence, clinical presentation, and severity of invasive pneumococcal disease (IPD)-causing serotypes and the impact of the 13-valent pneumococcal conjugate vaccination during epidemic and nonepidemic influenza periods in Catalonia, Spain. This was a prospective study in persons aged
Source: Journal of Clinical Microbiology - July 26, 2019 Category: Microbiology Authors: Hernandez, S., Munoz-Almagro, C., Ciruela, P., Soldevila, N., Izquierdo, C., Codina, M. G., Diaz, A., Moraga-Llop, F., Garcia-Garcia, J. J., Dominguez, A., Working Group of Projects PI11/02081 and PI11/2345 Tags: Epidemiology Source Type: research

True Measles Cases Undetected by Reverse Transcription-PCR (RT-PCR): Effect of Genetic Variability on Assay Sensitivity Needs To Be Regularly Surveyed [Letter To The Editor]
(Source: Journal of Clinical Microbiology)
Source: Journal of Clinical Microbiology - July 26, 2019 Category: Microbiology Authors: Dina, J., Omnes, J., Vauloup-Fellous, C., Collet, L., Hamel, J., Antona, D., Hübschen, J. M., Ben Mamou, M., Vabret, A. Tags: Letter To The Editor Source Type: research

Francisella tularensis Periprosthetic Joint Infections Diagnosed with Growth in Cultures [Bacteriology]
Tularemia caused by Francisella tularensis is a zoonotic infection of the Northern Hemisphere that mainly affects the skin, lymph nodes, bloodstream, and lungs. Other manifestations of tularemia are very rare, especially those with musculoskeletal involvement. Presenting in 2016, we diagnosed two cases of periprosthetic knee joint infections (PJI) caused by Francisella tularensis in Europe (one in Switzerland and one in the Czech Republic). We found only two other PJI cases in the literature, another knee PJI diagnosed 1999 in Ontario, Canada, and one hip PJI in Illinois, USA, in 2017. Diagnosis was made in all cases by po...
Source: Journal of Clinical Microbiology - July 26, 2019 Category: Microbiology Authors: Chrdle, A., Trnka, T., Musil, D., Fucentese, S. F., Bode, P., Keller, P. M., Achermann, Y. Tags: Bacteriology Source Type: research

Genomic, Antimicrobial Resistance, and Public Health Insights into Enterococcus spp. from Australian Chickens [Clinical Veterinary Microbiology]
This study evaluated antimicrobial resistance (AMR) of five enterococcal species isolated from Australian meat chickens, genomic features of Enterococcus faecium and Enterococcus faecalis, and the phylogenetic relationship of the poultry-derived E. faecium with isolates from human sepsis cases. All enterococcal isolates from chicken ceca were subjected to antimicrobial susceptibility testing. E. faecium and E. faecalis underwent whole-genome sequencing. E. faecium was compared at the core genome level to a collection of human isolates (n = 677) obtained from cases of sepsis over a 2-year period spanning 2015 to 2016. Overa...
Source: Journal of Clinical Microbiology - July 26, 2019 Category: Microbiology Authors: ODea, M., Sahibzada, S., Jordan, D., Laird, T., Lee, T., Hewson, K., Pang, S., Abraham, R., Coombs, G. W., Harris, T., Pavic, A., Abraham, S. Tags: Clinical Veterinary Microbiology Source Type: research

Comparison of the Novel Immunocatch Legionella Test with Sofia Legionella FIA Assay and with BinaxNOW Legionella Card Assay for Detection of Legionella pneumophila (Serogroup 1) Antigen in Urine Samples [Bacteriology]
In this study, a recently introduced immunochromatographic test (Immunocatch Legionella; Eiken Chemical Co., Ltd.) for Legionella pneumophila (serogroup 1) urinary antigen detection was compared with the Sofia Legionella fluorescent immunoassay (FIA) (Quidel) (routinely used in our laboratory) and with the widely used BinaxNOW Legionella assay (Alere). A total of 248 urine samples (60 frozen and 188 fresh) were evaluated. All of the samples were collected from patients with high clinical suspicion of Legionnaires’ disease. The three assays were performed simultaneously according to the manufacturers’ instructio...
Source: Journal of Clinical Microbiology - July 26, 2019 Category: Microbiology Authors: Congestri, F., Morotti, M., Vicari, R., Pedna, M. F., Sparacino, M., Torri, A., Bertini, S., Sambri, V. Tags: Bacteriology Source Type: research

Calibration and Evaluation of Quantitative Antibody Titers for Varicella-Zoster Virus by Use of the BioPlex 2200 [Immunoassays]
Most commercially available enzyme immunoassay-based methods have limited sensitivity to detect antibody responses to varicella-zoster virus (VZV) in vaccinated individuals, who produce lower antibody levels than those with natural infection. However, more sensitive methods are either not commercially available or less amenable to high-throughput testing. The BioPlex 2200 measles, mumps, rubella, and varicella (MMRV) IgG assay (Bio-Rad Laboratories, Hercules, CA) is an automated high-throughput platform based on the microsphere Luminex technology that measures antibodies against measles, mumps, rubella, and varicella virus...
Source: Journal of Clinical Microbiology - July 26, 2019 Category: Microbiology Authors: McLachlan, E., Scholz, H., Bolotin, S., Crowcroft, N. S., Hatchette, T. F., Jackson, C., Severini, A., on behalf of the Immunity of Canadians and Risk of Epidemics (iCARE) Laboratory Group and the Canadian Immunization Research Network (CIRN) Tags: Immunoassays Source Type: research

Detailed Analysis of the Characteristics of Sample Volume in Blood Culture Bottles [Bacteriology]
Blood volume is the most important variable for the detection of microorganisms in blood cultures (BCs). Most standards recommend 40 to 60 ml blood, collected in several BC bottles filled up to 10 ml. We measured blood volume in individual BC bottles and analyzed the associations of hospital, bottle type, day of the week, daily sampling time, and age and sex of the patient with sampling volume and BC result. The variation in blood volume per BC bottle was analyzed in a mixed linear model using hospital, bottle type, weekday, sampling time, age, and sex as fixed factors and patient identification (ID) and episode as random ...
Source: Journal of Clinical Microbiology - July 26, 2019 Category: Microbiology Authors: Henning, C., Aygül, N., Dinnetz, P., Wallgren, K., Özenci, V. Tags: Bacteriology Source Type: research

Design and Validation of Transcription-Mediated-Amplification Nucleic Acid Amplification Tests for Mycoplasma genitalium [Bacteriology]
Mycoplasma genitalium is a sexually transmitted bacterium linked to adverse sexual and reproductive health outcomes in women and men. M. genitalium is difficult to culture, and in the absence of validated amplified molecular methods for diagnosis of infection, there is no reference standard available for use as a comparator for the validation of new M. genitalium diagnostic tests. We evaluated the analytical and clinical performance of three transcription-mediated amplification (TMA) tests for M. genitalium, each targeting unique rRNA sequences, for use as a composite comparator for clinical validation of the Aptima Mycopl...
Source: Journal of Clinical Microbiology - July 26, 2019 Category: Microbiology Authors: Kirkconnell, B., Weinbaum, B., Santos, K., Le Nguyen, T., Vinluan, B., Astete, S., Wood, G. E., Totten, P. A., Getman, D. K. Tags: Bacteriology Source Type: research

Practical Guidance to Implementing Quality Management Systems in Public Health Laboratories Performing Next-Generation Sequencing: Personnel, Equipment, and Process Management (Phase 1) [Minireviews]
Quality standards as part of an effective quality management system (QMS) are the cornerstone for generating high-quality test results. Next-generation sequencing (NGS) has the potential to improve both clinical diagnostics and public health surveillance efforts in multiple areas, including infectious diseases. However, the laboratories adopting NGS methods face significant challenges due to the complex and modular process design. This document summarizes the first phase of quality system guidance developed by the Centers for Disease Control and Prevention (CDC) NGS Quality Workgroup. The quality system essentials of perso...
Source: Journal of Clinical Microbiology - July 26, 2019 Category: Microbiology Authors: Hutchins, R. J., Phan, K. L., Saboor, A., Miller, J. D., Muehlenbachs, A., on behalf of the CDC NGS Quality Workgroup Tags: Minireviews Source Type: research

Implications of Bacteriophage- and Bacteriophage Component-Based Therapies for the Clinical Microbiology Laboratory [Minireviews]
Treatment of bacterial infections is increasingly challenged by resistance to currently available antibacterial agents. Not only are such agents less likely to be active today than they were in the past, but their very use has selected for and continues to select for further resistance. Additional strategies for the management of bacterial illnesses must be identified. In this review, bacteriophage-based therapies are presented as one promising approach. In anticipation of their potential expansion into clinical medicine, clinical microbiologists may wish to acquaint themselves with bacteriophages and their antibacterial c...
Source: Journal of Clinical Microbiology - July 26, 2019 Category: Microbiology Authors: Caflisch, K. M., Patel, R. Tags: Minireviews Source Type: research

"Switching Partners": Piperacillin-Avibactam Is a Highly Potent Combination against Multidrug-Resistant Burkholderia cepacia Complex and Burkholderia gladioli Cystic Fibrosis Isolates [Bacteriology]
In persons with cystic fibrosis (CF), airway infection with Burkholderia cepacia complex (Bcc) species or Burkholderia gladioli presents a significant challenge due to inherent resistance to multiple antibiotics. Two chromosomally encoded inducible β-lactamases, a Pen-like class A and AmpC are produced in Bcc and B. gladioli. Previously, ceftazidime-avibactam demonstrated significant potency against Bcc and B. gladioli isolated from the sputum of individuals with CF; however, 10% of the isolates tested resistant to ceftazidime-avibactam. Here, we describe an alternative antibiotic combination to overcome ceftazidime-a...
Source: Journal of Clinical Microbiology - July 26, 2019 Category: Microbiology Authors: Zeiser, E. T., Becka, S. A., Wilson, B. M., Barnes, M. D., LiPuma, J. J., Papp-Wallace, K. M. Tags: Bacteriology Source Type: research

Real-Time PCR Assay for Differentiation of Typhoidal and Nontyphoidal Salmonella [Bacteriology]
Rapid and accurate differentiation of Salmonella spp. causing enteric fever from nontyphoidal Salmonella is essential for clinical management of cases, laboratory risk management, and implementation of public health measures. Current methods used for confirmation of identification, including biochemistry and serotyping as well as whole-genome sequencing analyses, take several days. Here we report the development and evaluation of a real-time PCR assay that can be performed directly on crude DNA extracts from bacterial colonies for the rapid identification of typhoidal and nontyphoidal Salmonella. (Source: Journal of Clinical Microbiology)
Source: Journal of Clinical Microbiology - July 26, 2019 Category: Microbiology Authors: Nair, S., Patel, V., Hickey, T., Maguire, C., Greig, D. R., Lee, W., Godbole, G., Grant, K., Chattaway, M. A. Tags: Bacteriology Source Type: research

Direct Detection of Pyrazinamide Resistance in Mycobacterium tuberculosis by Use of pncA PCR Sequencing [Mycobacteriology and Aerobic Actinomycetes]
An in-house-developed pncA sequencing assay for analysis of pyrazinamide (PZA) resistance was evaluated using 162 archived Mycobacterium tuberculosis complex (MTBC) isolates with phenotypic PZA susceptibility profiles that were well defined by analysis of Bactec MGIT 960 PZA kit and PZase activity data. Preliminary results showed 100% concordance between pncA sequencing and phenotypic PZA drug susceptibility test (DST) results among archived isolates. Also, 637 respiratory specimens were prospectively collected, and 158 were reported as MTBC positive by the Abbott Realtime MTB assay (96.3% sensitivity [95% confidence inter...
Source: Journal of Clinical Microbiology - July 26, 2019 Category: Microbiology Authors: Tam, K. K.-G., Leung, K. S.-S., Siu, G. K.-H., Chang, K.-C., Wong, S. S.-Y., Ho, P.-L., Leung, E. K.-C., Yam, W.-C. Tags: Mycobacteriology and Aerobic Actinomycetes Source Type: research

Characterization and Clinical Significance of Natural Variability in Hepatitis B Virus Reverse Transcriptase in Treatment-Naive Chinese Patients by Sanger Sequencing and Next-Generation Sequencing [Virology]
The objective of this study was to investigate the characterization and clinical significance of natural variability in HBV RT in treatment-naive patients. HBV RT sequences were analyzed in 427 patients by Sanger sequencing and in 66 patients by next-generation sequencing. Primary or secondary NA resistance (NAr) mutations were not found, except A181T in RT (rtA181T) by Sanger sequencing, but they were detected by next-generation sequencing. Mutations were found in 56 RT amino acid (aa) sites by Sanger sequencing, 36 of which had mutations that could lead to changes in B or T cell epitopes in the RT or S protein. The distr...
Source: Journal of Clinical Microbiology - July 26, 2019 Category: Microbiology Authors: Fu, Y., Zeng, Y., Chen, T., Chen, H., Lin, N., Lin, J., Liu, X., Huang, E., Wu, S., Wu, S., Xu, S., Wang, L., Ou, Q. Tags: Virology Source Type: research

Looking Backward To Move Forward: the Utility of Sequencing Historical Bacterial Genomes [Minireviews]
Many pathogens that caused devastating disease throughout human history, such as Yersinia pestis, Mycobacterium tuberculosis, and Mycobacterium leprae, remain problematic today. Historical bacterial genomes represent a unique source of genetic information and advancements in sequencing technologies have allowed unprecedented insights from this previously understudied resource. This minireview brings together example studies which have utilized ancient DNA, individual historical isolates (both extant and dead) and collections of historical isolates. The studies span human history and highlight the contribution that sequenci...
Source: Journal of Clinical Microbiology - July 26, 2019 Category: Microbiology Authors: Bennett, R. J., Baker, K. S. Tags: Minireviews Source Type: research

Editorial Board [Masthead]
(Source: Journal of Clinical Microbiology)
Source: Journal of Clinical Microbiology - July 26, 2019 Category: Microbiology Tags: Masthead Source Type: research

Don't Get Wound Up: Revised Fluoroquinolone Breakpoints for Enterobacteriaceae and Pseudomonas aeruginosa [Minireviews]
Fluoroquinolones remain some of the more commonly prescribed antimicrobial agents in the United States, despite the wide array of reported side effects that are associated with their use. In 2019, the Clinical and Laboratory Standards Institute revised the fluoroquinolone antimicrobial susceptibility testing breakpoints for both Enterobacteriaceae and Pseudomonas aeruginosa. This breakpoint revision was deemed necessary on the basis of pharmacokinetic and pharmacodynamic analyses suggesting that the previous breakpoints were too high, in addition to the inability of the previous breakpoints to detect low-level resistance t...
Source: Journal of Clinical Microbiology - June 25, 2019 Category: Microbiology Authors: Van, T. T., Minejima, E., Chiu, C. A., Butler-Wu, S. M. Tags: Minireviews Source Type: research

Epidemiology and Antifungal Susceptibility Profile of Aspergillus Species: Comparison between Environmental and Clinical Isolates from Patients with Hematologic Malignancies [Mycology]
This study was conducted as part of the Catholic Hematology Hospital Fungi Epidemiology (CAFÉ) study. A total of 207 proven/probable invasive aspergillosis and 102 clinical and 129 environmental Aspergillus isolates were included in this analysis. The incidence of proven/probable invasive aspergillosis was 1.3 cases/1,000 patient-days during the study period. Cryptic Aspergillus species accounted for 33.8%, with no differences in proportions between the clinical and environmental isolates. Section Nigri presented a high proportion (70.5%) of cryptic species, mainly from A. tubingensis and A. awamori: the former bein...
Source: Journal of Clinical Microbiology - June 25, 2019 Category: Microbiology Authors: Cho, S.-Y., Lee, D.-G., Kim, W.-B., Chun, H.-S., Park, C., Myong, J.-P., Park, Y.-J., Choi, J.-K., Lee, H.-J., Kim, S.-H., Park, S. H., Choi, S.-M., Choi, J.-H., Yoo, J.-H. Tags: Mycology Source Type: research

Molecular Bacterial Load Assay Concurs with Culture on NaOH-Induced Loss of Mycobacterium tuberculosis Viability [Mycobacteriology and Aerobic Actinomycetes]
Effective methods to detect viable Mycobacterium tuberculosis, the main causative agent of tuberculosis (TB), are urgently needed. To date, cultivation of M. tuberculosis is the gold standard, which depends on initial sample processing with N-acetyl-l-cysteine–sodium hydroxide (NALC-NaOH), chemicals that compromise M. tuberculosis viability and, consequently, the performance of downstream tests. We applied culture and the novel molecular bacterial load assay (MBLA) to measure the loss of M. tuberculosis viability following NALC-NaOH treatment of M. tuberculosis H37Rv pure culture and clinical sputum samples from pulm...
Source: Journal of Clinical Microbiology - June 25, 2019 Category: Microbiology Authors: Mtafya, B., Sabiiti, W., Sabi, I., John, J., Sichone, E., Ntinginya, N. E., Gillespie, S. H. Tags: Mycobacteriology and Aerobic Actinomycetes Source Type: research

Reduced Incubation Time of the Modified Carbapenem Inactivation Test and Performance of Carbapenem Inactivation in a Set of Carbapenemase-Producing Enterobacteriaceae with a High Proportion of blaIMP Isolates [Bacteriology]
Accurate and timely identification of carbapenemase-producing Enterobacteriaceae (CPE) is critical for microbiology laboratories in order to facilitate infection prevention, reduce the spread of multiresistant Gram-negative bacilli, and reduce delays to effective antibiotic therapy. We undertook a study to compare the carbapenem inactivation method (CIM) against the modified carbapenem inactivation method (mCIM) on a broad range of CPE isolates from Australia, including a high proportion of blaIMP isolates. Furthermore, we evaluated the performance of the mCIM with a reduced incubation time using automated incubation and d...
Source: Journal of Clinical Microbiology - June 25, 2019 Category: Microbiology Authors: Beresford, R. W., Maley, M. Tags: Bacteriology Source Type: research

Helicobacter pylori Mutations Detected by Next-Generation Sequencing in Formalin-Fixed, Paraffin-Embedded Gastric Biopsy Specimens Are Associated with Treatment Failure [Bacteriology]
In this study, formalin-fixed, paraffin-embedded (FFPE) gastric biopsy specimens from a cohort of individuals from northern Ohio in the United States were examined using a next-generation sequencing (NGS) assay to detect H. pylori mutations that are known to confer resistance to clarithromycin, levofloxacin, and tetracycline. From January 2016 to January 2017, 133 H. pylori-infected gastric biopsy specimens were identified histologically and subsequently analyzed by NGS to detect mutations in gyrA, 23S rRNA, and 16S rRNA genes. The method successfully detected H. pylori in 126 of 133 cases (95% sensitivity). Mutations conf...
Source: Journal of Clinical Microbiology - June 25, 2019 Category: Microbiology Authors: Nezami, B. G., Jani, M., Alouani, D., Rhoads, D. D., Sadri, N. Tags: Bacteriology Source Type: research

Closing the Brief Case: A Fatal Case of Necrotizing Fasciitis Due to Multidrug-Resistant Acinetobacter baumannii [The Brief Case]
(Source: Journal of Clinical Microbiology)
Source: Journal of Clinical Microbiology - June 25, 2019 Category: Microbiology Authors: Matthews, L., Goodrich, J. S., Weber, D. J., Bergman, N. H., Miller, M. B. Tags: The Brief Case Source Type: research

The Brief Case: A Fatal Case of Necrotizing Fasciitis Due to Multidrug-Resistant Acinetobacter baumannii [The Brief Case]
(Source: Journal of Clinical Microbiology)
Source: Journal of Clinical Microbiology - June 25, 2019 Category: Microbiology Authors: Matthews, L., Goodrich, J. S., Weber, D. J., Bergman, N. H., Miller, M. B. Tags: The Brief Case Source Type: research

Pathotyping the Zoonotic Pathogen Streptococcus suis: Novel Genetic Markers To Differentiate Invasive Disease-Associated Isolates from Non-Disease-Associated Isolates from England and Wales [Clinical Veterinary Microbiology]
We describe evaluation of our pathotyping tool, using an out-of-sample collection of 50 previously uncharacterized S. suis isolates, in comparison to existing methods used to characterize and subtype S. suis isolates. In doing so, we show our pathotyping approach to be a competitive method to characterize S. suis isolates recovered from pigs on UK farms and one that can easily be updated to incorporate global strain collections. (Source: Journal of Clinical Microbiology)
Source: Journal of Clinical Microbiology - June 25, 2019 Category: Microbiology Authors: Wileman, T. M., Weinert, L. A., Howell, K. J., Wang, J., Peters, S. E., Williamson, S. M., Wells, J. M., Langford, P. R., Rycroft, A. N., Wren, B. W., Maskell, D. J., Tucker, A. W., on behalf of the BRaDP1T Consortium Tags: Clinical Veterinary Microbiology Source Type: research

A TaqMan Probe-Based Real-Time PCR Assay for the Rapid Identification of the Emerging Multidrug-Resistant Pathogen Candida auris on the BD Max System [Mycology]
Candida auris is an emerging multidrug-resistant fungal pathogen that has been associated with nosocomial bloodstream and deep wound infections causing a high mortality rate mainly in intensive care unit (ICU) patients. Laboratories currently rely on phenotypic testing using commercial automated systems for identification of yeasts; however, this technique has often led to misidentification of C. auris to other closely related species. We developed and validated a TaqMan-based real-time PCR assay on the BD Max platform targeting ribosomal DNA (rDNA) region nucleotide sequences to quickly and accurately test for C. auris in...
Source: Journal of Clinical Microbiology - June 25, 2019 Category: Microbiology Authors: Lima, A., Widen, R., Vestal, G., Uy, D., Silbert, S. Tags: Mycology Source Type: research

Answer to July 2019 Photo Quiz [Photo Quiz]
(Source: Journal of Clinical Microbiology)
Source: Journal of Clinical Microbiology - June 25, 2019 Category: Microbiology Authors: Ortiz, D. A., Ren, P. Tags: Photo Quiz Source Type: research

Photo Quiz: A Multifocal Rash in a 16-Year-Old Aspiring Veterinarian [Photo Quiz]
(Source: Journal of Clinical Microbiology)
Source: Journal of Clinical Microbiology - June 25, 2019 Category: Microbiology Authors: Ortiz, D. A., Ren, P. Tags: Photo Quiz Source Type: research

Correction for Cannon et al., "Genetic and Epidemiologic Trends of Norovirus Outbreaks in the United States from 2013 to 2016 Demonstrated Emergence of Novel GII.4 Recombinant Viruses" [Author Correction]
(Source: Journal of Clinical Microbiology)
Source: Journal of Clinical Microbiology - June 25, 2019 Category: Microbiology Authors: Cannon, J. L., Barclay, L., Collins, N. R., Wikswo, M. E., Castro, C. J., Magana, L. C., Gregoricus, N., Marine, R. L., Chhabra, P., Vinje, J. Tags: Author Correction Source Type: research

The New, New Daptomycin Breakpoint for Enterococcus spp. [Commentary]
In 2019, the Clinical and Laboratory Standards Institute revised the daptomycin breakpoints for Enterococcus spp. twice in rapid succession. Analyses leading to these revisions included review of testing issues, murine and human in vivo pharmacodynamics, safety of off-label doses, and treatment outcomes. The data review brought up a dilemma that is encountered with increasing frequency: a breakpoint supported by pharmacokinetic/pharmacodynamic modeling that bisected the wild-type Enterococcus faecium MIC distribution. In such instances, not only does the probability of pharmacokinetic/pharmacodynamic targets need to be tak...
Source: Journal of Clinical Microbiology - June 25, 2019 Category: Microbiology Authors: Humphries, R. M. Tags: Commentary Source Type: research

Can You Speciate This for Me? A Micro-Comic Strip [Editorial]
(Source: Journal of Clinical Microbiology)
Source: Journal of Clinical Microbiology - June 25, 2019 Category: Microbiology Authors: Westblade, L. F., Nussbaum, A. J., McAdam, A. J. Tags: Editorial Source Type: research

Diagnosing and Managing Sepsis by Probing the Host Response to Infection: Advances, Opportunities, and Challenges [Minireviews]
Sepsis is a major source of mortality and morbidity globally. Accurately diagnosing sepsis remains challenging due to the heterogeneous nature of the disease, and delays in diagnosis and intervention contribute to high mortality rates. Measuring the host response to infection enables more rapid diagnosis of sepsis than is possible through direct detection of the causative pathogen, and recent advances in host response diagnostics and prognostics hold promise for improving outcomes. The current review discusses recent advances in the technologies used to probe the host response to infection, particularly those based on tran...
Source: Journal of Clinical Microbiology - June 25, 2019 Category: Microbiology Authors: Gunsolus, I. L., Sweeney, T. E., Liesenfeld, O., Ledeboer, N. A. Tags: Minireviews Source Type: research

CIM City: the Game Continues for a Better Carbapenemase Test [Commentary]
The Clinical and Laboratory Standards Institute and European Committee on Antimicrobial Susceptibility Testing agree that carbapenemase testing is not necessary for clinical care, provided that the laboratory is up to date with current breakpoints. Nonetheless, publication on the development and modification of carbapenemase tests continues, as is the case in this issue of the Journal of Clinical Microbiology (R. W. Beresford and M. Maley, J Clin Microbiol 57:e01852-18, 2019, https://doi.org/10.1128/JCM.01852-18). This commentary explores modifications to the carbapenem inactivation method—but is this the right focus...
Source: Journal of Clinical Microbiology - June 25, 2019 Category: Microbiology Authors: Humphries, R. M. Tags: Commentary Source Type: research

Whole-Genome Single-Nucleotide Polymorphism (SNP) Analysis Applied Directly to Stool for Genotyping Shiga Toxin-Producing Escherichia coli: an Advanced Molecular Detection Method for Foodborne Disease Surveillance and Outbreak Tracking [Bacteriology]
Whole-genome sequencing (WGS) of pathogens from pure culture provides unparalleled accuracy and comprehensive results at a cost that is advantageous compared with traditional diagnostic methods. Sequencing pathogens directly from a primary clinical specimen would help circumvent the need for culture and, in the process, substantially shorten the time to diagnosis and public health reporting. Unfortunately, this approach poses significant challenges because of the mixture of multiple sequences from a complex fecal biomass. The aim of this project was to develop a proof of concept protocol for the sequencing and genotyping o...
Source: Journal of Clinical Microbiology - June 25, 2019 Category: Microbiology Authors: Singh, N., Lapierre, P., Quinlan, T. M., Halse, T. A., Wirth, S., Dickinson, M. C., Lasek-Nesselquist, E., Musser, K. A. Tags: Bacteriology Source Type: research

Storage of Sputum in Cetylpyridinium Chloride, OMNIgene.SPUTUM, and Ethanol Is Compatible with Molecular Tuberculosis Diagnostic Testing [Mycobacteriology and Aerobic Actinomycetes]
We compared cetylpyridinium chloride (CPC), ethanol (ETOH), and OMNIgene.SPUTUM (OMNI) for 28-day storage of sputum at ambient temperature before molecular tuberculosis diagnostics. Three sputum samples were collected from each of 133 smear-positive tuberculosis (TB) patients (399 sputum samples). Each patient’s sputum was stored with either CPC, ETOH, or OMNI for 28 days at ambient temperature, with subsequent rpoB amplification targeting a short fragment (81 bp, GeneXpert MTB/RIF [Xpert]) or a long fragment (1,764 bp, in-house nested PCR). For 36 patients, Xpert was also performed at baseline on all 108 fresh sputu...
Source: Journal of Clinical Microbiology - June 25, 2019 Category: Microbiology Authors: Sanoussi, C. N., de Jong, B. C., Affolabi, D., Meehan, C. J., Odoun, M., Rigouts, L. Tags: Mycobacteriology and Aerobic Actinomycetes Source Type: research

Development of an Enzyme-Linked Immunosorbent Assay for Rapid Detection of Dengue Virus (DENV) NS1 and Differentiation of DENV Serotypes during Early Infection [Virology]
In this study, we developed an enzyme-linked immunosorbent assay (ELISA) for the detection of dengue virus (DENV) NS1 by pairing a serotype-cross-reactive monoclonal antibody (MAb) with one of four serotype-specific MAbs in order to facilitate the rapid detection of NS1 antigens and the simultaneous differentiation of DENV serotypes. A total of 146 serum samples obtained from patients suspected to be in the acute phase of DENV infection were used to evaluate the clinical application of our novel test for the detection and serotyping of DENV. The overall sensitivity rate of our test was 84.85%, and the sensitivity rates for...
Source: Journal of Clinical Microbiology - June 25, 2019 Category: Microbiology Authors: Lai, S.-C., Huang, Y.-Y., Shu, P.-Y., Chang, S.-F., Hsieh, P.-S., Wey, J.-J., Tsai, M.-H., Ben, R.-J., Hsu, Y.-M., Fang, Y.-C., Hsiao, M.-L., Lin, C.-C. Tags: Virology Source Type: research

Simple Assay for Detection of the Central Asia Outbreak Clade of the Mycobacterium tuberculosis Beijing Genotype [Mycobacteriology and Aerobic Actinomycetes]
The Central Asia outbreak (CAO) clade is a branch of the Mycobacterium tuberculosis Beijing genotype that is associated with multidrug resistance, increased transmissibility, and epidemic spread in parts of the former Soviet Union. Furthermore, migration flows bring these strains far beyond their areas of origin. We aimed to find a specific molecular marker of the Beijing CAO clade and develop a simple and affordable method for its detection. Based on the bioinformatics analysis of the large M. tuberculosis whole-genome sequencing (WGS) data set (n = 1,398), we identified an IS6110 insertion in the Rv1359-Rv1360 intergenic...
Source: Journal of Clinical Microbiology - June 25, 2019 Category: Microbiology Authors: Shitikov, E., Vyazovaya, A., Malakhova, M., Guliaev, A., Bespyatykh, J., Proshina, E., Pasechnik, O., Mokrousov, I. Tags: Mycobacteriology and Aerobic Actinomycetes Source Type: research